Dissecting the Satellite DNA Landscape in Three CactophilicDrosophilaSequenced Genomes

Abstract

Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA) which are among the most abundant, fast evolving (yet poorly studied) genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198) and two novel ones (CDSTR138 and CDSTR130). Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis. Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis) and CDSTR198 (in D. buzzatii) in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9–2.9%) within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.

Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex

“…gambiae will contribute to higher genetic differentiation, and will eventually lead to postzygotic reproductive isolation between some populations of these important disease vectors. Extensive studies of Drosophila species show that heterochromatin, in general, and satellite DNA, in particular, can be a source of tremendous genetic variation [76][77][78][79][80]. Heterochromatin can also modulate differential gene expression and cause variable phenotypes, including differences in immune response [81,82].…”

Satellite DNA: An Evolving Topic

“…Thus, short arrays of satDNAs dispersed along the euchromatin have been described. There are also satDNAs present not exclusively within heterochromatin but also dispersed as single repeats or short arrays within euchromatin [ 14 , 21 , 80 , 85 , 127 , 128 , 129 , 130 , 131 ]. Similarly, shorter repeats showed the same capability to cluster both in euchromatin and in heterochromatin.…”

“…Different arrays on the same or in different chromosomes may experience independent homogenization for arrays- or chromosome-specific repeat variants [ 122 , 127 , 131 , 201 ]. Thus, the analysis of euchromatic and heterochromatic repeats from 52 arrays showed that the homogenization of satDNA repeats of the 1688 satDNA family of Drosophila occurred differentially for distinct genomic regions, from euchromatin to heterochromatin and from local arrays to chromosomes [ 127 ].…”

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

“…The data generated is now being used to determine satDNA sequences organization in the genome [95], explore predicted evolutionary patterns and hypothesis (e.g., [35,68,96,97]), as well as to shed light into the function of these sequences [81,98]. We are now closer than ever to fully access the sequence information hidden within repetitive-rich chromosome structures like centromeres and telomeres.…”